class: center, middle, inverse, title-slide # Computing in R ## AMC Graduate School ### Perry Moerland ### 2019-01-24 (updated: 2019-02-25) --- background-image: url(https://upload.wikimedia.org/wikipedia/commons/thumb/1/1b/R_logo.svg/500px-R_logo.svg.png) background-size: cover ??? Image credit: [Wikimedia Commons](https://commons.wikimedia.org/wiki/File:Sharingan_triple.svg) --- # Course setup - Course aim: become familiar with the basics of R - Two days, two sessions per day: 9:30-12:30 & 13:30-16:30 - Mix of interactive lectures and computer exercises -- - [Course website](http://wiki.bioinformaticslaboratory.nl/foswiki/bin/view/BioLab/ComputinginR) .footnote[ [1] http://wiki.bioinformaticslaboratory.nl/foswiki/bin/view/BioLab/ComputinginR ] -- - Comments and suggestions for improvement are most welcome --- # Stages in statistical analysis 1. <span style="color:red">Importing</span> data into statistical program 1. <span style="color:red">Inspecting</span> data - finding errors, cleaning - recoding and transforming - describing and summarizing data using spreadsheets, tables and graphics 1. <span style="color:red">Analyzing</span> data: estimation, uncertainty (confidence intervals, p-value), predictive value 1. <span style="color:red">Validating</span> model <br> Check the assumptions of the model 1. <span style="color:red">Reporting</span> of results <br> summary, tables, graphics <br> export --- # R as a pocket calculator - First of all, R can be used as a pocket calculator - Many mathematical operations are pre-defined in R <br> ```r > 2+7 ``` ``` # [1] 9 ``` -- ```r > sqrt(2) ``` ``` # [1] 1.414214 ``` ```r > cos(pi) ``` ``` # [1] -1 ``` ```r > log10(10^3) ``` ``` # [1] 3 ``` --- # Matrices .left-column[  ] .right-column[ ```r A <- matrix(data = 1:9, nrow = 3, ncol = 3) A[2,] ``` ``` # [1] 2 5 8 ``` ```r A[,1] ``` ``` # [1] 1 2 3 ``` ```r A[2,3] ``` ``` # [1] 8 ``` ] --- # Constructing a data frame ```r > pclass <- c("1st","2nd","1st") > survived <- c(1,1,0) > name <- c("Elisabeth Walton","Hudson Trevor","Helen Loraine") > age <- c(29.0,0.9167,2.0) > titanic <- data.frame(pclass,survived,name,age) > titanic ``` ``` # pclass survived name age # 1 1st 1 Elisabeth Walton 29.0000 # 2 2nd 1 Hudson Trevor 0.9167 # 3 1st 0 Helen Loraine 2.0000 ``` --- # R plots ```r > par(mar = c(4, 4, 1, .1)) > x <- (0:100)/10 > plot(x, x^3 - 13 * x^2 + 39 * x) ``` <!-- --> --- # Enhancing a plot .pull-left[ ```r x<-(0:100)/10 plot(x,x^3-13*x^2+39*x, type="l", xlab="time (hours)", ylab="temperature", cex.axis=1.5,cex.lab=1.5) ``` ] .pull-right[  ] --- # Enhancing a plot .pull-left[ ```r x<-(0:100)/10 plot(x,x^3-13*x^2+39*x, type="l", xlab="time (hours)", ylab="temperature", cex.axis=1.5,cex.lab=1.5) *points(2,34,col="red",pch=16, * cex=2) ``` ] .pull-right[  ] --- # Enhancing a plot .pull-left[ ```r x<-(0:100)/10 plot(x,x^3-13*x^2+39*x, type="l", xlab="time (hours)", ylab="temperature", cex.axis=1.5,cex.lab=1.5) points(2,34,col="red",pch=16, cex=2) *arrows(4,50,2.2,34.5) ``` ] .pull-right[  ] --- # Enhancing a plot .pull-left[ ```r x<-(0:100)/10 plot(x,x^3-13*x^2+39*x, type="l", xlab="time (hours)", ylab="temperature", cex.axis=1.5,cex.lab=1.5) points(2,34,col="red",pch=16, cex=2) arrows(4,50,2.2,34.5) *text(4.15,50,"local maximum", * adj=0,col="blue",cex=1.5) ``` ] .pull-right[  ] --- # Enhancing a plot .pull-left[ ```r x<-(0:100)/10 plot(x,x^3-13*x^2+39*x, type="l", xlab="time (hours)", ylab="temperature", cex.axis=1.5,cex.lab=1.5) points(2,34,col="red",pch=16, cex=2) arrows(4,50,2.2,34.5) text(4.15,50,"local maximum", adj=0,col="blue",cex=1.5) *lines(x,30-50*sin(x/2), * col="blue") ``` ] .pull-right[  ] --- # Enhancing a plot .pull-left[ ```r x<-(0:100)/10 plot(x,x^3-13*x^2+39*x, type="l", xlab="time (hours)", ylab="temperature", cex.axis=1.5,cex.lab=1.5) points(2,34,col="red",pch=16, cex=2) arrows(4,50,2.2,34.5) text(4.15,50,"local maximum", adj=0,col="blue",cex=1.5) lines(x,30-50*sin(x/2), col="blue") *legend(x=0,y=80, * legend=c("Sahara", * "Gobi"), * lty=1, * col=c("black","blue"), * cex=1.5) * ``` ] .pull-right[  ] --- # Interactive plots ```r > library(plotly) > dat = data.frame(x=(0:100)/10,y=x^3-13*x^2+39*x) > plot_ly(data=dat,x=~x,y=~y) ``` <div id="htmlwidget-586897067a9f2189d7c5" style="width:504px;height:288px;" class="plotly html-widget"></div> <script type="application/json" data-for="htmlwidget-586897067a9f2189d7c5">{"x":{"visdat":{"fb02dd13c8f":["function () ","plotlyVisDat"]},"cur_data":"fb02dd13c8f","attrs":{"fb02dd13c8f":{"x":{},"y":{},"alpha_stroke":1,"sizes":[10,100],"spans":[1,20]}},"layout":{"margin":{"b":40,"l":60,"t":25,"r":10},"xaxis":{"domain":[0,1],"automargin":true,"title":"x"},"yaxis":{"domain":[0,1],"automargin":true,"title":"y"},"hovermode":"closest","showlegend":false},"source":"A","config":{"modeBarButtonsToAdd":[{"name":"Collaborate","icon":{"width":1000,"ascent":500,"descent":-50,"path":"M487 375c7-10 9-23 5-36l-79-259c-3-12-11-23-22-31-11-8-22-12-35-12l-263 0c-15 0-29 5-43 15-13 10-23 23-28 37-5 13-5 25-1 37 0 0 0 3 1 7 1 5 1 8 1 11 0 2 0 4-1 6 0 3-1 5-1 6 1 2 2 4 3 6 1 2 2 4 4 6 2 3 4 5 5 7 5 7 9 16 13 26 4 10 7 19 9 26 0 2 0 5 0 9-1 4-1 6 0 8 0 2 2 5 4 8 3 3 5 5 5 7 4 6 8 15 12 26 4 11 7 19 7 26 1 1 0 4 0 9-1 4-1 7 0 8 1 2 3 5 6 8 4 4 6 6 6 7 4 5 8 13 13 24 4 11 7 20 7 28 1 1 0 4 0 7-1 3-1 6-1 7 0 2 1 4 3 6 1 1 3 4 5 6 2 3 3 5 5 6 1 2 3 5 4 9 2 3 3 7 5 10 1 3 2 6 4 10 2 4 4 7 6 9 2 3 4 5 7 7 3 2 7 3 11 3 3 0 8 0 13-1l0-1c7 2 12 2 14 2l218 0c14 0 25-5 32-16 8-10 10-23 6-37l-79-259c-7-22-13-37-20-43-7-7-19-10-37-10l-248 0c-5 0-9-2-11-5-2-3-2-7 0-12 4-13 18-20 41-20l264 0c5 0 10 2 16 5 5 3 8 6 10 11l85 282c2 5 2 10 2 17 7-3 13-7 17-13z m-304 0c-1-3-1-5 0-7 1-1 3-2 6-2l174 0c2 0 4 1 7 2 2 2 4 4 5 7l6 18c0 3 0 5-1 7-1 1-3 2-6 2l-173 0c-3 0-5-1-8-2-2-2-4-4-4-7z m-24-73c-1-3-1-5 0-7 2-2 3-2 6-2l174 0c2 0 5 0 7 2 3 2 4 4 5 7l6 18c1 2 0 5-1 6-1 2-3 3-5 3l-174 0c-3 0-5-1-7-3-3-1-4-4-5-6z"},"click":"function(gd) { \n // is this being viewed in RStudio?\n if (location.search == '?viewer_pane=1') {\n alert('To learn about plotly for collaboration, visit:\\n https://cpsievert.github.io/plotly_book/plot-ly-for-collaboration.html');\n } else {\n window.open('https://cpsievert.github.io/plotly_book/plot-ly-for-collaboration.html', '_blank');\n }\n }"}],"cloud":false},"data":[{"x":[0,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1,1.1,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,2,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,3,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8,3.9,4,4.1,4.2,4.3,4.4,4.5,4.6,4.7,4.8,4.9,5,5.1,5.2,5.3,5.4,5.5,5.6,5.7,5.8,5.9,6,6.1,6.2,6.3,6.4,6.5,6.6,6.7,6.8,6.9,7,7.1,7.2,7.3,7.4,7.5,7.6,7.7,7.8,7.9,8,8.1,8.2,8.3,8.4,8.5,8.6,8.7,8.8,8.9,9,9.1,9.2,9.3,9.4,9.5,9.6,9.7,9.8,9.9,10],"y":[0,3.771,7.288,10.557,13.584,16.375,18.936,21.273,23.392,25.299,27,28.501,29.808,30.927,31.864,32.625,33.216,33.643,33.912,34.029,34,33.831,33.528,33.097,32.544,31.875,31.096,30.213,29.232,28.159,27,25.761,24.448,23.067,21.624,20.125,18.576,16.983,15.352,13.689,12,10.291,8.56800000000004,6.83699999999999,5.10400000000001,3.375,1.65600000000003,-0.0470000000000539,-1.72800000000001,-3.381,-5,-6.57900000000004,-8.11200000000002,-9.59300000000005,-11.016,-12.375,-13.664,-14.877,-16.008,-17.051,-18,-18.8489999999999,-19.592,-20.2230000000001,-20.736,-21.125,-21.384,-21.507,-21.4879999999999,-21.321,-21,-20.519,-19.872,-19.053,-18.056,-16.875,-15.5040000000001,-13.9370000000001,-12.168,-10.191,-8,-5.58900000000006,-2.95200000000011,-0.08299999999997,3.02400000000011,6.375,9.976,13.833,17.9520000000001,22.3390000000001,27,31.9410000000001,37.1680000000001,42.6870000000001,48.5039999999998,54.625,61.0559999999999,67.8029999999999,74.8720000000001,82.269,90],"type":"scatter","mode":"markers","marker":{"color":"rgba(31,119,180,1)","line":{"color":"rgba(31,119,180,1)"}},"error_y":{"color":"rgba(31,119,180,1)"},"error_x":{"color":"rgba(31,119,180,1)"},"line":{"color":"rgba(31,119,180,1)"},"xaxis":"x","yaxis":"y","frame":null}],"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.2,"selected":{"opacity":1},"debounce":0},"base_url":"https://plot.ly"},"evals":["config.modeBarButtonsToAdd.0.click"],"jsHooks":[]}</script> --- # Tables If you want to generate a table, make sure it is in .HTML format (instead of Markdown or other formats), e.g., ```r > library(foreign) > titanic3 <- read.dta("Exercises/titanic3.dta") > knitr::kable(head(titanic3[,1:6],n=5), format = "html") ``` <table> <thead> <tr> <th style="text-align:left;"> pclass </th> <th style="text-align:right;"> survived </th> <th style="text-align:left;"> name </th> <th style="text-align:left;"> sex </th> <th style="text-align:right;"> age </th> <th style="text-align:right;"> sibsp </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> 1st </td> <td style="text-align:right;"> 1 </td> <td style="text-align:left;"> Allen, Miss. Elisabeth Walton </td> <td style="text-align:left;"> female </td> <td style="text-align:right;"> 29.0000 </td> <td style="text-align:right;"> 0 </td> </tr> <tr> <td style="text-align:left;"> 1st </td> <td style="text-align:right;"> 1 </td> <td style="text-align:left;"> Allison, Master. Hudson Trevor </td> <td style="text-align:left;"> male </td> <td style="text-align:right;"> 0.9167 </td> <td style="text-align:right;"> 1 </td> </tr> <tr> <td style="text-align:left;"> 1st </td> <td style="text-align:right;"> 0 </td> <td style="text-align:left;"> Allison, Miss. Helen Loraine </td> <td style="text-align:left;"> female </td> <td style="text-align:right;"> 2.0000 </td> <td style="text-align:right;"> 1 </td> </tr> <tr> <td style="text-align:left;"> 1st </td> <td style="text-align:right;"> 0 </td> <td style="text-align:left;"> Allison, Mr. Hudson Joshua Crei </td> <td style="text-align:left;"> male </td> <td style="text-align:right;"> 30.0000 </td> <td style="text-align:right;"> 1 </td> </tr> <tr> <td style="text-align:left;"> 1st </td> <td style="text-align:right;"> 0 </td> <td style="text-align:left;"> Allison, Mrs. Hudson J C (Bessi </td> <td style="text-align:left;"> female </td> <td style="text-align:right;"> 25.0000 </td> <td style="text-align:right;"> 1 </td> </tr> </tbody> </table> --- # HTML Widgets ```r > DT::datatable( + head(titanic3[,1:6],n=100), + fillContainer = FALSE, options = list(pageLength = 3) + ) ``` <div id="htmlwidget-eb056e0a869931761296" style="width:100%;height:auto;" class="datatables html-widget"></div> <script type="application/json" data-for="htmlwidget-eb056e0a869931761296">{"x":{"filter":"none","fillContainer":false,"data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","23","24","25","26","27","28","29","30","31","32","33","34","35","36","37","38","39","40","41","42","43","44","45","46","47","48","49","50","51","52","53","54","55","56","57","58","59","60","61","62","63","64","65","66","67","68","69","70","71","72","73","74","75","76","77","78","79","80","81","82","83","84","85","86","87","88","89","90","91","92","93","94","95","96","97","98","99","100"],["1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st","1st"],[1,1,0,0,0,1,1,0,1,0,0,1,1,1,1,0,0,1,1,0,1,1,1,1,1,0,1,1,1,1,0,1,1,1,0,1,1,1,0,0,0,1,1,1,1,0,0,1,1,1,1,0,0,0,1,1,1,1,0,1,0,1,0,1,1,1,1,1,1,1,0,0,1,1,0,0,1,0,1,1,0,0,1,1,0,1,1,1,1,0,1,1,1,1,1,1,0,1,1,1],["Allen, Miss. 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